Re: [AMBER] ensuring lack of non-equilibrium jolt on restart

From: David Case <>
Date: Sun, 18 Dec 2016 08:52:09 -0500

On Fri, Dec 16, 2016, Neale, Christopher Andrew wrote:
> I am running a standard simulation with amber. The first segment was run
> for 8 microseconds. After about 2 microseconds I observed the formation
> of a salt-bridge that remained stable until the end of the first 8
> microsecond segment. Upon restarting, this salt bridge is stable for the
> first 1 nanosecond but breaks after 1.6 nanoseconds. I realize that this
> could just be a coincidence and that the trajectories are stochastic,
> but I wanted to check to see if anybody can take a look at my -i input
> file to see if I did something that could have jolted the system at the
> beginning of the restart (stable for 6 us and then breaking in less than
> 1/1000th of that time immediately after a restart).

You should always set ig=-1 for Langevin dynamics. This is the default for
Amber16, but not for earlier versions of the code.

Since the thermostat will change on every run, an easy thing is just to
restart again after the 8 microsec, and see if the salt bridge breaks again
very early on. But 1.6 nsec is actually a rather long time (microscopically),
so any "jolt" at restart ought to have disspated into heat long before that.


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Received on Sun Dec 18 2016 - 06:00:05 PST
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